Tags : Browse Projects

Select a tag to browse associated projects and drill deeper into the tag cloud.

The Chemistry Development Kit

Compare

  Analyzed 3 months ago

The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.

569K lines of code

13 current contributors

3 months since last commit

6 users on Open Hub

Activity Not Available
4.33333
   
I Use This

Bioclipse

Compare

  Analyzed 12 months ago

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from ... [More] Eclipse, such as help system, software updates, preferences, cross-platform deployment etc. [Less]

1.13M lines of code

12 current contributors

almost 6 years since last commit

5 users on Open Hub

Activity Not Available
4.66667
   
I Use This

Blue Obelisk

Compare

  Analyzed 4 months ago

The Internet has brought together a group of chemists/programmers/informaticians who are driven by wanting to do things better, but are frustrated with the Closed systems that chemists currently have to work with. They share a belief in the concepts of Open Source, Open Standards and Open Data ... [More] (but not necessarily Open Access). And they express this in code, data, algorithms, specifications, tutorials, demonstrations, articles and anything that helps get the message across. [Less]

98.2K lines of code

0 current contributors

over 6 years since last commit

2 users on Open Hub

Activity Not Available
5.0
 
I Use This

OpenChrom

Compare

  Analyzed 5 months ago

OpenChrom offers an open source alternative to the ChemStation from Agilent Technologies to analyze mass spectrometric chromatographic data. Its focus is to handle data files from different LC/MS, GC/MS systems and vendors such as (*.D) chromatograms from Agilent, Finnigan ITS40 (*.ms) and ITDS ... [More] (*.dat), NetCDF (*.cdf), MzXML (*.mzxml), CSV (*.csv) and other formats. Preprocessing steps are supported by applying filter, for instance to remove certain ions (m/z) such as nitrogen (28) or water (18). Classifier allow to characterize chromatograms. Extensions are appreciated and can be easily integrated since OpenChrom is open source and uses a modular and flexible approach, which allows other developers to implement their own methods, algorithms, classifier, filter, detectors or integrators. [Less]

401K lines of code

15 current contributors

6 months since last commit

1 users on Open Hub

Activity Not Available
5.0
 
I Use This
Licenses: Apache-2.0, BSD-4-Cla..., EPL-1.0

RDKit

Compare

  Analyzed 4 days ago

A collection of cheminformatics and machine-learning software written in C++ and Python.

191K lines of code

0 current contributors

about 4 years since last commit

1 users on Open Hub

Inactive
0.0
 
I Use This
Licenses: BSD-3-Clause, GPL-2.0+

JaCuda

Compare

  Analyzed 4 days ago

JaCuda is a small project which provides several mathematical function useful for a chemist or somebody working with mass specs. These functions will be executed using a cuda compatible gpu or if none is available it will fall back to the c++ implementation. If this is also not possible we will ... [More] invoke the function defined in the programming language. Which would be java/groovy for now and later python. --this project is abounded for the benefit of pycuda-- [Less]

1.8K lines of code

0 current contributors

almost 9 years since last commit

1 users on Open Hub

Inactive
0.0
 
I Use This

cinfony

Compare

  Analyzed about 2 years ago

CinfonyCinfony presents a common API to several cheminformatics toolkits. It uses the Python programming language, and builds on top of OpenBabel, RDKit and the CDK. DocumentationThe Cinfony paper Install on Windows or Linux A complete description of Cinfony API documentation. This ... [More] documentation can also be accessed using the help command, e.g. help(cdk). Further information on Pybel and using the OpenBabel Python bindings is available on the OpenBabel wiki ExampleHere's a short example to get the juices flowing. Let's read a molecule with OpenBabel, use Webel to find out its IUPAC name, draw it with RDKit and calculate descriptor values with the CDK: C:\> cinfony # Set environment variables C:\> python Python 2.6.4 (r264:75708, Oct 26 2009, 08:23:19) [MSC v.1500 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information. >>> from cinfony import rdk, cdk, obabel, webel >>> obabelmol = obabel.readstring("smi", "CCC") >>> print webel.Molecule(obabelmol).write("iupac") "PROPANE" >>> rdkmol = rdk.Molecule(obabelmol) >>> rdkmol.draw(show=False, filename="propane.png") >>> print cdk.Molecule(rdkmol).calcdesc() {'chi0C': 2.7071067811865475, 'BCUT.4': 4.4795252101839402, 'BCUT.5': 5.14569107 34650307, 'BCUT.2': -0.17199466342172476, 'BCUT.3': 0.048131793579068549, 'BCUT. 0': 11.889999999999995, 'BCUT.1': 12.110018178813911, 'rotatableBondsCount': 2, 'mde.9': 0.0, 'mde.8': 0.0, 'mde.3': 0.0, 'mde.2': 0.0, ... } [Less]

2.96K lines of code

0 current contributors

about 7 years since last commit

1 users on Open Hub

Activity Not Available
0.0
 
I Use This

Toxtree (Toxic Hazard Estimation )

Compare

  Analyzed almost 3 years ago

Description Estimates toxic hazard of chemical compounds. The latest version includes the following toxicity prediction modules: -Cramer rules (oral toxicity) -Toxicity mode of action via Verhaar scheme -Skin irritation prediction -Eye irritation prediction -Benigni / Bossa rulebase for ... [More] mutagenicity and carcinogenicity prediction -START biodegradation and persistence prediction -Structure Alerts for identification of Michael Acceptors -Structure Alerts for skin sensitisation -Kroes TTC Decision tree -SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and metabolites prediction -Structure Alerts for the in vivo micronucleus assay in rodents (ISSMIC) -Structural Alerts for Functional Group Identification (ISSFUNC) Pplugin framework to incorporate different approaches. [Less]

382K lines of code

1 current contributors

almost 3 years since last commit

0 users on Open Hub

Activity Not Available
0.0
 
I Use This

ChemClipse

Compare

  Analyzed 5 months ago

Provide the chemical world with a frontend for entering and managing chemical data. This frontend will be made with the Eclipse Rich Client Platform. Additionally a Server component will be developed for storing and retrieving the data.

375K lines of code

6 current contributors

10 months since last commit

0 users on Open Hub

Activity Not Available
0.0
 
I Use This
Licenses: No declared licenses

chemojava

Compare

  Analyzed about 1 year ago

ChemoJava is a project based on the Chemistry Development Kit (LGPL). It aggregates chemoinformatics functionality which itself is license GPL, but using the CDK APIs. It is not aimed at replacing the CDK, but complementing it with unique functionality, possibly from originally other projects, which is not available from the CDK itself.

3.74K lines of code

0 current contributors

about 8 years since last commit

0 users on Open Hub

Activity Not Available
0.0
 
I Use This